Sodium in PDB 5ob8: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl):
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl), PDB code: 5ob8 was solved by N.Pontillo, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	55.56 / 1.85
*Space group*	P 4₃ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	78.573, 78.573, 36.664, 90.00, 90.00, 90.00
*R / R_free (%)*	16 / 23

Other elements in 5ob8:

Ruthenium	(Ru)	2 atoms
Chlorine	(Cl)	3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl) (pdb code 5ob8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl), PDB code: 5ob8:

Sodium binding site 1 out of 1 in 5ob8

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Sodium Binding Sites List in 5ob8

Sodium binding site 1 out of 1 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na203 b:45.9 occ:1.00	O	A:SER60	2.2	32.1	1.0
	O	A:HOH392	2.2	32.4	1.0
	O	A:HOH365	2.4	27.6	1.0
	O	A:CYS64	2.4	22.8	1.0
	O	A:ARG73	2.5	51.3	1.0
	OG	A:SER72	2.6	56.4	1.0
	C	A:SER60	3.3	29.7	1.0
	C	A:CYS64	3.5	26.7	1.0
	CB	A:SER72	3.6	51.8	1.0
	C	A:ARG73	3.6	41.9	1.0
	CA	A:SER60	3.9	26.9	1.0
	CA	A:ASN65	4.0	26.4	1.0
	N	A:ARG73	4.1	41.1	1.0
	CB	A:SER60	4.1	25.6	1.0
	N	A:ASN65	4.2	26.0	1.0
	C	A:SER72	4.3	49.5	1.0
	N	A:ARG61	4.4	32.1	1.0
	C	A:ARG61	4.5	36.6	1.0
	CA	A:ARG73	4.5	41.2	1.0
	N	A:ASN74	4.5	32.8	1.0
	N	A:CYS64	4.5	26.9	1.0
	CB	A:THR69	4.6	29.6	1.0
	N	A:ASP66	4.6	28.6	1.0
	CL	A:CL204	4.6	39.7	1.0
	OD1	A:ASN65	4.6	30.3	1.0
	O	A:ARG61	4.6	40.7	1.0
	CA	A:SER72	4.6	48.2	1.0
	CA	A:ASN74	4.6	30.7	1.0
	CA	A:ARG61	4.7	39.4	1.0
	CA	A:CYS64	4.7	28.3	1.0
	O	A:SER72	4.7	46.5	1.0
	CB	A:ASN74	4.8	34.3	1.0
	CB	A:ASN65	4.8	24.6	1.0
	C	A:ASN65	4.8	22.5	1.0
	N	A:TRP62	4.8	30.1	1.0
	OG	A:SER60	4.9	23.2	1.0
	O	A:THR69	5.0	27.7	1.0
	OG1	A:THR69	5.0	23.3	1.0

Reference:

N.Pontillo, G.Ferraro, L.Messori, G.Tamasi, A.Merlino. Ru-Based Co Releasing Molecules with Azole Ligands: Interaction with Proteins and the Co Release Mechanism Disclosed By X-Ray Crystallography. Dalton Trans V. 46 9621 2017.
ISSN: ESSN 1477-9234
PubMed: 28702564
DOI: 10.1039/C7DT01991B

Page generated: Mon Oct 7 23:09:52 2024

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